MRMFeaturePickerFile Class Reference

MRMFeaturePickerFile loads components and components groups parameters from a .csv file. More...

#include <OpenMS/FORMAT/MRMFeaturePickerFile.h>

Inheritance diagram for MRMFeaturePickerFile:

Collaboration diagram for MRMFeaturePickerFile:

Public Member Functions
	MRMFeaturePickerFile ()=default
	Constructor. More...
	~MRMFeaturePickerFile () override=default
	Destructor. More...
void	load (const String &filename, std::vector< MRMFeaturePicker::ComponentParams > &cp_list, std::vector< MRMFeaturePicker::ComponentGroupParams > &cgp_list)
	Loads the file's data and saves it into vectors of ComponentParams and ComponentGroupParams. More...
Public Member Functions inherited from CsvFile
	CsvFile ()
	Default constructor. More...
	~CsvFile () override
	destructor More...
	CsvFile (const String &filename, char is=',', bool ie=false, Int first_n=-1)
	Constructor with filename. More...
void	load (const String &filename, char is=',', bool ie=false, Int first_n=-1)
	Loads data from a text file. More...
void	store (const String &filename)
	Stores the buffer's content into a file. More...
void	addRow (const StringList &list)
	Add a row to the buffer. More...
void	clear ()
	Clears the buffer. More...
bool	getRow (Size row, StringList &list) const
	writes all items from a row to list More...
std::vector< String >::size_type	rowCount () const
	Returns the number of rows that were loaded from the file. More...

Protected Member Functions
bool	extractParamsFromLine_ (const StringList &line, const std::map< String, Size > &headers, MRMFeaturePicker::ComponentParams &cp, MRMFeaturePicker::ComponentGroupParams &cgp) const
	Extracts the information from a StringList and saves it into the correct data structures. More...
void	setCastValue_ (const String &key, const String &value, Param &params) const
	Helper method which takes care of converting the given value to the desired type, based on the header (here key) information. More...

Detailed Description

MRMFeaturePickerFile loads components and components groups parameters from a .csv file.

The structures defined in MRMFeaturePicker are used.

It is required that columns component_name and component_group_name are present. Lines whose component_name's or component_group_name's value is an empty string, will be skipped. The class supports the absence of information within other columns.

A reduced example of the expected format (fewer columns are shown here):

component_name,component_group_name,TransitionGroupPicker:stop_after_feature,TransitionGroupPicker:PeakPickerChromatogram:sgolay_frame_length arg-L.arg-L_1.Heavy,arg-L,2,15 arg-L.arg-L_1.Light,arg-L,2,17 orn.orn_1.Heavy,orn,3,21 orn.orn_1.Light,orn,3,13

Constructor & Destructor Documentation

MRMFeaturePickerFile()

MRMFeaturePickerFile ( )

default

Constructor.

~MRMFeaturePickerFile()

~MRMFeaturePickerFile ( )

overridedefault

Destructor.

Member Function Documentation

extractParamsFromLine_()

bool extractParamsFromLine_ ( const StringList &  line, const std::map< String, Size > &  headers, MRMFeaturePicker::ComponentParams &  cp, MRMFeaturePicker::ComponentGroupParams &  cgp  ) const

protected

Extracts the information from a StringList and saves it into the correct data structures.

Parameters

[in]	line	The line parsed from the input file
[in]	headers	A mapping from a given header to its value's position
[out]	cp	The extracted component parameters
[out]	cgp	The extracted component group parameters

Returns

Returns false if component_name or component_group_name are empty strings. Otherwise, it returns true.

load()

void load	(	const String &	filename,
		std::vector< MRMFeaturePicker::ComponentParams > &	cp_list,
		std::vector< MRMFeaturePicker::ComponentGroupParams > &	cgp_list
	)

Loads the file's data and saves it into vectors of ComponentParams and ComponentGroupParams.

The file is expected to contain at least two columns: component_name and component_group_name. Otherwise, an exception is thrown.

If a component group (identified by its name) is found multiple times, only the first one is saved.

Parameters

[in]	filename	Path to the .csv input file
[out]	cp_list	Component params are saved in this list
[out]	cgp_list	Component Group params are saved in this list

Exceptions

Exception::MissingInformation	If the required columns are not found.
Exception::FileNotFound	If input file is not found.

setCastValue_()

void setCastValue_ ( const String &  key, const String &  value, Param &  params  ) const

protected

Helper method which takes care of converting the given value to the desired type, based on the header (here key) information.

Parameters

[in]	key	The header name with which the correct conversion is chosen
[in]	value	The value to be converted
[in,out]	params	The object where the new value is saved